Advanced experiences: O Scientific packages, e.g. Turbomole, Gaussian03, Dylax, DFTB+, gDFTB, ATK, Wien2k, NAMD, AutoDock, and ImageJ O Computer programming, e.g. FORTRAN, C/C++, Java, Tcl, and Python O Parallel programming, e.g. OpenMP O Web programming, e.g. javascript, ASP, ADO, and PHP O Markup languages, e.g. HTML, CSS, XML, LaTeX, and FarsiTex O Database management systems, e.g. MySQL, Microsoft SQL server, and MS Access O Web design applications, e.g. MS FrontPage and Macromedia DreamWeaver O Math applications, e.g. Mathematica O Graphics applications, e.g. Adobe PhotoShop and CorelDraw O Plotting applications, e.g. Xmgrace, Gnuplot, SigmaPlot, Origin, and GraphPad Prism O Network administration (Linux, Windows Server) O Hardware assembling O Some experiences: MPI, UML, Perl, Matlab, and Adobe Premiere.
My first experience in computer programing goes back to 1992 when I was a high school student. I started with BASIC-A and GW-BASIC, along with BATCH scripting for the operating system MS-DOS 3. Couple of years later, I learned programming with C and working with NetWare computer networks. I learned also to work with small databanks based on dBase and FoxPro. After entering the university, I started to learn FORTRAN IV and FORTRAN 77, and working with UNIX operating system. During my Bachelor’s studies, I learned also web scripting with HTML, CSS, XML, and javascript, and later, programming with ASP, ADO, and PHP together with working with large databanks based on MS-SQL and MySQL. I improved also my knowledge of different computer languages, e.g. C/C++, FORTRAN 90/95, along with experiences in Java, Perl and Python. Meanwhile, I had the chance to learn installing and maintaining Windows- and Linux-based networks. Later, during my Master’s studies, I was attending the graduate course of parallel programming, held for the graduate students of software engineering.
I was the teaching assistant of the course “Computational Physics” for the undergraduate students. and working part-time as network administrator of the advanced studies computer site of the Faculty of Physics of Isfahan University of Technology. Besides, I was working as freelance software- and web-developer on several projects, e.g. web-based databank programs, remote control programs, and e-learning platforms. I was also responsible for setting up and maintaining a high-performance computer cluster, based on AMD Opteron Cluster with InfiniBand technology, at the Center of Microtechnologies in TU-Chemnitz.
My scientific computing experiences were expanded more to the field of materials science during my doctoral studies in TU-Chemnitz, including writing codes for computing the tight-binding electronic configuration of clusters, the vibrational modes and vibronic couplings of molecules, and the resistivity in thin metal films and metal nanowires based on the Mayadas-Shatzkes model.
Since joining the MPI-PKS, I have worked on developing a proper computer application initially for simulating active liquid crystals as a model for studying the length- and shape-controlled meiotic spindle, a bipolar assembly of motor proteins and microtubules, which are polymerizing proteins with a cylindrical structure, during the cell division. The core part of the software has been written in FORTRAN 2003, containing over 30,000 code lines and parallelized with OpenMP. Through a Tcl interface, the software is able to communicate with VMD in order to demonstrate parts of the results.
Besides, in collaboration with the Division of Immunopathology of the Nervous System of the Institute of Neuropathology of the University Hospital of Tübingen, I have developed computer programs based on classical Monte Carlo and the steepest descent optimization method in order to perform computer simulations describing the patterns of histone acetylation in response to medical drugs, along with the distribution of HDACs in the brain.
Last update: May 1, 2014